6-125695434-G-C

Variant names:

• chr6-125695434-G-C
• rs13328298
• ENST00000423208.2:n.202+11755G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000423208.2(LINC02523):​n.202+11755G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: LINC02523 ENST00000423208.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 8 publications found

Genes affected

LINC02523 (HGNC:53542): (long intergenic non-protein coding RNA 2523)

HEY2-AS1 (HGNC:55652): (HEY2 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423208.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02523	NR_038906.1		n.202+11755G>C		intron	N/A
	HEY2-AS1	NR_183490.1		n.682+24990C>G		intron	N/A
	HEY2-AS1	NR_183491.1		n.551+24990C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02523	ENST00000423208.2	TSL:1	n.202+11755G>C		intron	N/A
	HEY2-AS1	ENST00000427852.7	TSL:3	n.273+24990C>G		intron	N/A
	HEY2-AS1	ENST00000451660.6	TSL:3	n.443+24990C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 2021

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13328298; hg19: chr6-126016580;